NEW YORK (GenomeWeb News) – A team at the Fred Hutchinson Cancer Research Center has won $4.4 million in funding from the National Cancer Institute to use RNA sequencing to study proteins that may be involved in the body's immune response to cancer, the center said on Monday.
The aim is to tackle a big challenge facing the cancer research community: how to identify the immunogenic proteins in tumors that generate responses from patients' immune systems, enabling them to better fight off cancers. The investigators also want to differentiate these proteins from those found in healthy tissue.
While many cancers are able to suppress the human immune system, new research has shown that a number of advanced lung cancer patients overcome this and improve dramatically when they are treated with drugs that prevent T-cell inhibition.
"It is clear that a number of people have mounted an immune response to lung and other cancers and these new therapies allow the T cells to do their job better," Laura Chow, a University of Washington assistant professor, said in a statement.
"It would help improve our ability to understand how cancer avoids immune surveillance and also design better treatment and prevention strategies if we knew which proteins were being recognized by T cells," said Chow, who is currently running clinical trials with the Seattle Cancer Care Alliance aimed at testing this approach.
The NCI-funded project at Fred Hutch that aims to address this problem will be headed by Martin McIntosh, who runs the Computational Biology Program.
"What we're doing is finding what could be hundreds of possible cancer-specific proteins, but we do not know whether they are likely to be useful for immune-based therapy until we find out whether the body recognizes them as foreign," McIntosh explained.
"We do this by experimentally testing each predicted protein to see if we can observe an immune response in a cancer patient whose tumor harbors one of these proteins. Experimental verification is necessary because, although the Human Genome Project can guide us to what a healthy genome sequence looks like, there is no existing data resource yet telling us what proteins exist, or do not exist, in the body of a healthy individual," he said.
McIntosh's team will sequence RNAs that are actively being translated into proteins and then integrate their findings with public data from large-scale studies, such as The Cancer Genome Atlas, to try to predict which of these proteins are unique to cancer cells and to identify the immune repertoire for ovarian, lung, and other cancers.